Mutagenetix > Incidental Mutation

Incidental Mutation 'BB009:Pcdhga1'

642561

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga1

Ensembl Gene

ENSMUSG00000103144

Gene Name

protocadherin gamma subfamily A, 1

Synonyms

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

BB009

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37794846-37974926 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 37796513 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 506 (S506P)

Ref Sequence

ENSEMBL: ENSMUSP00000142062 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000115661] [ENSMUST00000194190] [ENSMUST00000194544] [ENSMUST00000194888]

AlphaFold

Q91XZ0

Predicted Effect

probably benign
Transcript: ENSMUST00000115661

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

Domain	Start	End	E-Value	Type
CA	20	131	5.3e-2	SMART
CA	155	240	1.51e-19	SMART
CA	264	348	7.6e-25	SMART
CA	372	453	1.42e-24	SMART
CA	477	563	1.42e-24	SMART
CA	594	674	4.12e-12	SMART
low complexity region	706	721	N/A	INTRINSIC
Pfam:Cadherin_tail	796	930	3.9e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably damaging
Transcript: ENSMUST00000194190
AA Change: S506P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144
AA Change: S506P

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	31	131	3.16e-2	SMART
CA	155	240	5.39e-16	SMART
CA	264	345	6.72e-26	SMART
CA	369	450	1.32e-24	SMART
CA	474	560	4.17e-22	SMART
CA	591	669	4.48e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	912	931	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194544

SMART Domains

Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

Domain	Start	End	E-Value	Type
Blast:CA	18	66	5e-20	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000194888
AA Change: S506P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144
AA Change: S506P

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	31	131	1.6e-4	SMART
CA	155	240	2.7e-18	SMART
CA	264	345	3.3e-28	SMART
CA	369	450	6.7e-27	SMART
CA	474	560	2e-24	SMART
CA	591	669	2.2e-15	SMART
transmembrane domain	692	714	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null/reporter allele are viable and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss2	A	G	2: 155,415,100 (GRCm39)	R666G	unknown	Het
Adam21	T	A	12: 81,606,938 (GRCm39)	N275Y	probably damaging	Het
Arhgap24	A	T	5: 102,993,835 (GRCm39)		probably benign	Het
Arhgef1	C	T	7: 24,619,135 (GRCm39)	L459F	probably damaging	Het
Bbx	A	T	16: 50,030,806 (GRCm39)		probably null	Het
Blk	C	T	14: 63,611,008 (GRCm39)	G445S	possibly damaging	Het
Brca1	T	C	11: 101,430,843 (GRCm39)	E33G	possibly damaging	Het
Cacna1s	T	G	1: 136,012,097 (GRCm39)	L513R	probably damaging	Het
Cnn3	T	A	3: 121,245,078 (GRCm39)	M98K	probably benign	Het
Cttnbp2	T	A	6: 18,427,532 (GRCm39)	L716F	probably damaging	Het
Dlgap1	A	T	17: 70,823,233 (GRCm39)	R73W	probably damaging	Het
Dnajc4	A	G	19: 6,965,638 (GRCm39)	L182P	probably damaging	Het
Dock2	T	C	11: 34,217,998 (GRCm39)	M1191V	probably benign	Het
Fam13a	C	T	6: 58,960,873 (GRCm39)		probably null	Het
Fbn2	C	T	18: 58,153,555 (GRCm39)	G2569E	possibly damaging	Het
Fes	T	C	7: 80,029,620 (GRCm39)	I623V	probably damaging	Het
Fyco1	A	C	9: 123,658,055 (GRCm39)	L707R	possibly damaging	Het
Gadd45b	T	A	10: 80,766,169 (GRCm39)	V7E	possibly damaging	Het
Gm19410	T	A	8: 36,262,753 (GRCm39)	C897S	probably damaging	Het
Hk1	A	G	10: 62,151,299 (GRCm39)	L31P	probably damaging	Het
Hoxa4	T	G	6: 52,167,397 (GRCm39)	K261N	probably damaging	Het
Hrh4	T	A	18: 13,148,869 (GRCm39)	L77*	probably null	Het
Igf1r	A	T	7: 67,861,802 (GRCm39)	I1121F	possibly damaging	Het
Igkv16-104	A	T	6: 68,402,778 (GRCm39)	I24L	probably benign	Het
Itk	A	T	11: 46,231,519 (GRCm39)	W346R	probably benign	Het
Kdm2a	A	G	19: 4,369,184 (GRCm39)	S1144P	probably damaging	Het
Krt86	A	T	15: 101,374,473 (GRCm39)	S289C	probably damaging	Het
Lonrf1	T	C	8: 36,690,070 (GRCm39)	I663V	probably benign	Het
Lrp2	T	G	2: 69,256,371 (GRCm39)	I4590L	probably benign	Het
Lrrc8d	C	T	5: 105,960,891 (GRCm39)	R434C	probably damaging	Het
Maneal	T	C	4: 124,755,638 (GRCm39)	Y108C	probably damaging	Het
Muc21	TCCTGAGGCAGTGCTGGATACAGGGGTGGTTGGGGTGGGTGAAGAGCCTGAGGCAGTGCTGGAT	TCCTGAGGCAGTGCTGGAT	17: 35,933,525 (GRCm39)		probably benign	Het
Myh8	G	A	11: 67,185,430 (GRCm39)	V894I	probably benign	Het
Ncam2	T	G	16: 81,412,708 (GRCm39)	L732R	probably damaging	Het
Nsun4	A	T	4: 115,901,997 (GRCm39)	D156E	probably damaging	Het
Or10z1	T	C	1: 174,078,260 (GRCm39)	I78V	probably benign	Het
Or1e23	A	C	11: 73,407,983 (GRCm39)	L14R	probably damaging	Het
Or2n1d	A	T	17: 38,646,146 (GRCm39)	I33L	probably benign	Het
Or5b106	A	T	19: 13,123,345 (GRCm39)	M226K	probably benign	Het
Or5v1b	T	C	17: 37,841,075 (GRCm39)	I69T	probably benign	Het
Or6c66	C	A	10: 129,461,094 (GRCm39)	V279F	probably damaging	Het
P2rx7	G	A	5: 122,782,245 (GRCm39)	V37I	probably benign	Het
Pcdh15	A	G	10: 74,481,359 (GRCm39)	R235G	probably benign	Het
Pira2	A	T	7: 3,845,435 (GRCm39)		probably null	Het
Plch1	A	G	3: 63,609,402 (GRCm39)	V935A	probably benign	Het
Plscr4	C	T	9: 92,372,843 (GRCm39)	R322*	probably null	Het
Prpf8	A	G	11: 75,383,423 (GRCm39)	D607G	possibly damaging	Het
Ptdss1	T	C	13: 67,114,496 (GRCm39)	W215R	probably damaging	Het
Ptpn9	C	A	9: 56,943,900 (GRCm39)	P258Q	possibly damaging	Het
Rfpl4b	A	G	10: 38,697,346 (GRCm39)	V85A	possibly damaging	Het
Sacs	C	A	14: 61,442,327 (GRCm39)	Q1458K	probably damaging	Het
Scfd2	A	T	5: 74,692,211 (GRCm39)	S24T	probably benign	Het
Siae	A	G	9: 37,544,980 (GRCm39)	D325G	probably benign	Het
Slc22a23	C	A	13: 34,366,960 (GRCm39)	A683S	probably damaging	Het
Slc44a3	A	T	3: 121,306,009 (GRCm39)	I244N	possibly damaging	Het
Srrm2	T	A	17: 24,037,501 (GRCm39)	S1382T	probably benign	Het
Tfap2c	A	G	2: 172,393,706 (GRCm39)	Y207C	probably damaging	Het
Timd5	C	A	11: 46,426,366 (GRCm39)	P158T	probably benign	Het
Tnc	T	C	4: 63,926,857 (GRCm39)	I890V	probably benign	Het
Trim30a	A	T	7: 104,078,545 (GRCm39)	I177N	probably benign	Het
Tshz2	T	A	2: 169,728,251 (GRCm39)	M949K	possibly damaging	Het
Ttn	T	G	2: 76,555,530 (GRCm39)	T30492P	probably damaging	Het
Ubb	C	T	11: 62,443,611 (GRCm39)	Q214*	probably null	Het
Ulk2	A	G	11: 61,698,916 (GRCm39)	S423P	probably benign	Het
Vmn1r237	C	A	17: 21,534,725 (GRCm39)	D149E	probably benign	Het
Zbtb24	A	G	10: 41,327,504 (GRCm39)	D130G	probably benign	Het
Zfp689	C	A	7: 127,043,523 (GRCm39)	G369V	probably damaging	Het
Zg16	A	G	7: 126,649,577 (GRCm39)	F128S	probably damaging	Het
Zmym1	T	G	4: 126,944,578 (GRCm39)	N203T	possibly damaging	Het

Other mutations in Pcdhga1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
BB019:Pcdhga1	UTSW	18	37,796,513 (GRCm39)	missense	probably damaging	1.00
R1074:Pcdhga1	UTSW	18	37,958,140 (GRCm39)	splice site	probably benign
R1869:Pcdhga1	UTSW	18	37,973,143 (GRCm39)	missense	probably damaging	0.98
R1871:Pcdhga1	UTSW	18	37,973,143 (GRCm39)	missense	probably damaging	0.98
R3723:Pcdhga1	UTSW	18	37,796,045 (GRCm39)	missense	possibly damaging	0.89
R3732:Pcdhga1	UTSW	18	37,797,176 (GRCm39)	missense	probably benign	0.00
R4243:Pcdhga1	UTSW	18	37,796,605 (GRCm39)	missense	probably damaging	1.00
R4245:Pcdhga1	UTSW	18	37,796,605 (GRCm39)	missense	probably damaging	1.00
R4424:Pcdhga1	UTSW	18	37,795,632 (GRCm39)	missense	probably damaging	0.97
R4898:Pcdhga1	UTSW	18	37,795,407 (GRCm39)	missense	possibly damaging	0.63
R4941:Pcdhga1	UTSW	18	37,795,659 (GRCm39)	missense	probably benign	0.10
R5021:Pcdhga1	UTSW	18	37,796,876 (GRCm39)	missense	probably damaging	1.00
R5765:Pcdhga1	UTSW	18	37,796,714 (GRCm39)	missense	probably benign	0.31
R6176:Pcdhga1	UTSW	18	37,797,282 (GRCm39)	missense	probably benign	0.22
R6380:Pcdhga1	UTSW	18	37,796,022 (GRCm39)	missense	probably damaging	1.00
R7062:Pcdhga1	UTSW	18	37,958,130 (GRCm39)	missense	probably damaging	1.00
R7146:Pcdhga1	UTSW	18	37,795,164 (GRCm39)	missense	probably benign	0.04
R7266:Pcdhga1	UTSW	18	37,973,028 (GRCm39)	missense	possibly damaging	0.94
R7525:Pcdhga1	UTSW	18	37,795,281 (GRCm39)	missense	probably damaging	1.00
R7553:Pcdhga1	UTSW	18	37,882,735 (GRCm39)	splice site	probably null
R7581:Pcdhga1	UTSW	18	37,795,230 (GRCm39)	missense	probably damaging	1.00
R7932:Pcdhga1	UTSW	18	37,796,513 (GRCm39)	missense	probably damaging	1.00
R8330:Pcdhga1	UTSW	18	37,796,376 (GRCm39)	missense	probably benign	0.19
R8385:Pcdhga1	UTSW	18	37,795,149 (GRCm39)	missense	probably damaging	1.00
R8549:Pcdhga1	UTSW	18	37,966,386 (GRCm39)	makesense	probably null
R9147:Pcdhga1	UTSW	18	37,796,433 (GRCm39)	missense	possibly damaging	0.54
R9148:Pcdhga1	UTSW	18	37,796,433 (GRCm39)	missense	possibly damaging	0.54
R9192:Pcdhga1	UTSW	18	37,973,084 (GRCm39)	missense	probably damaging	1.00
R9336:Pcdhga1	UTSW	18	37,795,251 (GRCm39)	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- AACAGATCAGGGAACTCCGC -3'
(R):5'- ATCTCTGGGGCATTGTCATTC -3'

Sequencing Primer
(F):5'- ACTGCTAGTGACAGATATCAATGAC -3'
(R):5'- CTGATCTATCATGAACAGACTCAGAG -3'

Posted On

2020-08-01